[Bio-Linux] help regarding BLAST running

[Tim Booth]

Hi Simon and Vijay,

I disagree with Simon - NR is a translated database so it is a peptide
DB and blastx is therefore appropriate for a nucleotide query.

Also, there is no reason to revert to the legacy "blastall" version of
BLAST, even though it is still available on Bio-Linux 7.

The only problem I can see is that your file name contains spaces.  This
is a bad idea as the shell has no way of knowing that the spaces are
part of the file name and assumes they are new parameters to the
command.  In this case you can put the file name in "quotes" but a
better idea is to ensure that your file names never contain spaces.

Does that fix it?

Cheers,

TIM

On Mon, 2013-02-04 at 11:21 +0000, Wagstaff, Simon wrote:
> Dear Vijay,
> 
> The problems are with your BLAST syntax. If you do a quick Google
> search you will find lots of web sites that will help you construct
> your BLAST search e.g.
> http://www.mathworks.co.uk/help/bioinfo/ref/blastlocal.html. You can
> also go to the NCBI documentation.
> 
>  
> 
> Parameters you need are:
> 
>  
> 
> -p program_name
> 
> -d database_name
> 
> -i input_sequence 
> 
> -e evalue (optional)
> 
> -o output_file
> 
>  
> 
> Looks me like you are searching nt query sequences against an nt
> database - if so blastx is also the wrong flavour of BLAST
> 
>  
> 
> You need something like this
> 
> blastall -p blastn -d my_database -i my_filename -e 0.1 -o
> my_output_file
> 
>  
> 
> Avoid underscores in your filenames as they will be misinterpreted but
> BLAST as command-line arguments - see your error below.
> 
>  
> 
> Simon
> 
>  
> 
> From: bio-linux-bounces at nebclists.nerc.ac.uk
> [mailto:bio-linux-bounces at nebclists.nerc.ac.uk] On Behalf Of Vijay
> Kumar
> Sent: 04 February 2013 10:09
> To: bio-linux at nebclists.nerc.ac.uk
> Subject: [Bio-Linux] help regarding BLAST running
> 
> 
>  
> 
> dear sir,
> 
> 
>  i am Dr.VIJAY using BIOLINUX 7 for last 2 months.its really working
> good for biologist with own PC.  now i face problem while working with
> BLAST run in terminal. when ever i run the BLAST i am getting error
> message like below for both single sequences and multiple sequences
> too. please help me( i am biology student, so i am not  exposure to
> linux commend and error problem.THANK U SIR
> 
> 
>  
> 
> 
>  
> 
> 
> vijayakumar at vijayakumar-SVE14112ENB[bioinf_files] blastx -db
> blastdb/nr.02 -query sra_data contig list - nucleotide_
> sequences.fasta -evalue 0.1 > vijay.blastx
> 
> 
> USAGE
> 
> 
>   blastx [-h] [-help] [-import_search_strategy filename]
> 
> 
>     [-export_search_strategy filename] [-db database_name]
> 
> 
>     [-dbsize num_letters] [-gilist filename] [-seqidlist filename]
> 
> 
>     [-negative_gilist filename] [-entrez_query entrez_query]
> 
> 
>     [-db_soft_mask filtering_algorithm] [-db_hard_mask
> filtering_algorithm]
> 
> 
>     [-subject subject_input_file] [-subject_loc range] [-query
> input_file]
> 
> 
>     [-out output_file] [-evalue evalue] [-word_size int_value]
> 
> 
>     [-gapopen open_penalty] [-gapextend extend_penalty]
> 
> 
>     [-xdrop_ungap float_value] [-xdrop_gap float_value]
> 
> 
>     [-xdrop_gap_final float_value] [-searchsp int_value]
> 
> 
>     [-max_hsps_per_subject int_value] [-frame_shift_penalty
> frameshift]
> 
> 
>     [-max_intron_length length] [-seg SEG_options]
> 
> 
>     [-soft_masking soft_masking] [-matrix matrix_name]
> 
> 
>     [-threshold float_value] [-culling_limit int_value]
> 
> 
>     [-best_hit_overhang float_value] [-best_hit_score_edge
> float_value]
> 
> 
>     [-window_size int_value] [-ungapped] [-lcase_masking] [-query_loc
> range]
> 
> 
>     [-strand strand] [-parse_deflines] [-query_gencode int_value]
> 
> 
>     [-outfmt format] [-show_gis] [-num_descriptions int_value]
> 
> 
>     [-num_alignments int_value] [-html] [-max_target_seqs
> num_sequences]
> 
> 
>     [-num_threads int_value] [-remote] [-version]
> 
> 
>  
> 
> 
> DESCRIPTION
> 
> 
>    Translated Query-Protein Subject BLAST 2.2.26+
> 
> 
>  
> 
> 
> Use '-help' to print detailed descriptions of command line arguments
> 
> 
> ========================================================================
> 
> 
> Error: (CArgException::eSynopsis) Too many positional arguments (1),
> the offending value: contig
> 
> 
> Error: (CArgException::eSynopsis) Application's initialization failed
> 
> 
> vijayakumar at vijayakumar-SVE14112ENB[bioinf_files]
> 
> 

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://nebc.nerc.ac.uk
+44 1491 69 2705